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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttgagatcactcagttttatgctacatttatgttctgtctcaataaaatttcttttgttctggttggctcttttgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG

Basic information

species Zea mays
transcript GRMZM5G814700_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
---------------gtatgttttgagatcactcagttttatgctacatttatgttctgtctcaataaaatttcttttgttctggttggctcttttgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG
               || |  |||  | ||| |   |||| |  | | |||   |||| | ||  | |  ||  | |  ||||  ||| ||   | || || |||||| ||||| ||||||||  | |||||||||||||||| |||||| || |||||||||||||||||| | |||||||| || |||
gtatgtgtaacaactgt-taatttaggttcattt--ttttttcttgcctttgccttct-tttctgtcattttcatgtatttctaattgact---tgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG

upper sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 3
----------gtatgttttgagat-cactcagttttatgctacatttatgttctgtctcaataaaatttcttttgttctggttggctcttttgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG
          | |  |   ||  |    |||||| ||  |  ||||||  |  | | |   | |||  ||||||  |  |  ||  | | |||  || ||||||||| ||||||||||| || ||||| ||||||||| | ||||  || |||||||||||| ||||  ||||||||||||| |  
agttttttctgaaaatgaagaattatgttcagttctacacctcatttacataattttttcttgaaacatctttttctgggactgatt-tgttgtcttgcagGTATACATCCAAGATGCTGTTAGCTGCAATTGATGAACGCCATAGAGGAACTTATGATTTTGTTTATCTGCCAATTGATTTCAGA

upper sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 11
-------gtatgttt-tgagatcactcagttttat-gct-acatttatgttctgtctcaataaaatttcttttgttctggttggctcttttgg--gtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG
        | | ||| ||   | || ||   | || ||| | |||  ||||   ||    |   ||||||    || || || | | |  |||   ||  |||||||| || || |||||  | ||||| |||||||||  ||||   || ||||||||||||||||| ||||||||||| || || 
cattcatttctatttgtggttttacacaccataattgctcagattcctgttgcatcctc-tgttatttctgcc-ttttgatttgatataatggtaattgtagGTATACTTCAAAAATGCTTCTTGCTGCAATTGATGAACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAA

upper sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 1
gtatgttttgagatcactcagttttatgctacatttatgttctgtctcaataaaatttcttttgttctggttggctcttttgg--gtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG
                                     ||||   ||    ||  ||||||    || || || | | |  |||   ||  |||||||| || || |||||  | ||| | |||||||||   |||   || ||||||||||||||||| ||||||||||| || || 
-------------------------------------tgttgcatcctc-tattatttctgcc-ttttgatttgatataatggtaattataggtatacttcaaaaatgcttcttgctacaattgatgaacaccattgagGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|22542340|gb|BU092793.1|BU092793
EST:     ACACTGATGATAAAGAATATCCCAAATAA                         GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
genomic: ACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
EST: gi|91877858|gb|EB407815.1|EB407815
EST:     CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAA                         GTATACCTCCCAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
genomic: CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
EST: gi|211008041|gb|FL362435.1|FL362435
EST:     CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAA                         GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
genomic: CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
EST: gi|71307207|gb|DR789770.1|DR789770
EST:     CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAA                         GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
genomic: CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
EST: gi|33093066|gb|CF053060.1|CF053060
EST:     CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAA                         GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
genomic: CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
EST: gi|32867814|gb|CF007496.1|CF007496
EST:     CGGGGGGAAGACTCACGAACTACACTCATGATAAAGAATATCCCAAATAA                         GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
genomic: CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
EST: gi|71772002|gb|DR969939.1|DR969939
EST:     CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAA                         GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
genomic: CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
EST: gi|32837478|gb|CD977156.1|CD977156
EST:     CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAA                         GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC
genomic: CGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 454

ACCAGTCTGATAATAAGCGGCAGTATGAGCTTGATGTTGACCGCATAATGCGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 354

ACCAGTCTGATAATAAGCGGCAGTATGAGCTTGATGTTGACCGCATAATGCGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 354

ACCAGTCTGATAATAAGCGGCAGTATGAGCTTGATGTTGACCGCATAATGCGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 514

ACCAGTCTGATAATAAGCGGCAGTATGAGCTTGATGTTGACCGCATAATGCGGGGGGAAGACTCACGAACTACACTGATGATAAAGAATATCCCAAATAAgtatgttttg ... tgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttctgtctcaataaaatttcttttgttctggttggctcttttgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG
                                       ctctttt  CT-rich tract
             aataaaatttcttttg  TA-rich tract